1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
|
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
import os
import unittest
import numpy
from cclib.bridge import cclib2openbabel
class OpenbabelTest(unittest.TestCase):
"""Tests for the cclib2openbabel bridge in cclib."""
def setUp(self):
self.path = os.path.abspath(os.path.dirname(__file__))
def test_makeopenbabel(self):
import openbabel
atomnos = numpy.array([1, 8, 1], "i")
atomcoords = numpy.array([[[-1., 1., 0.], [0., 0., 0.], [1., 1., 0.]]])
obmol = cclib2openbabel.makeopenbabel(atomcoords, atomnos)
obconversion = openbabel.OBConversion()
formatok = obconversion.SetOutFormat("inchi")
assert obconversion.WriteString(obmol).strip() == "InChI=1S/H2O/h1H2"
def test_readfile(self):
"""Try to load an XYZ file with uracyl through Openbabel"""
data = cclib2openbabel.readfile(self.path + "/uracil.xyz", "XYZ")
assert data.natom == 12
if __name__ == "__main__":
unittest.main()
|
